I ran all 3 wings of Flex SoO. I then got the quest to collect secret of the empire. My question is can I still kill those bosses in SoO for a shot at more secrets this week or is it one kill a week chance with or without the quest?

Rewriting this to make it clearer with how drops for Wrathion's Legendary drops work in Patch 5.4.

The chance for the item to drop is one attempt per eligible boss, per week across all difficulties.

The chance for the item to drop is the same regardless of difficulty mode.

Lei Shen and Sha of Pride are 100% guaranteed to drop the item that you need.

- Note: If you have already obtained a drop for a different item earlier in the week such as Secrets of the Empire, they will not drop a Titan Runestone if they are defeated again in the same week. For The Strength of One's Foes where you collect 10xSigil of Power and 10xSigil of Wisdom they can drop from bosses in the following locations:

Mogu'shan Vaults

Heart of Fear

Terrace of Endless Spring

Throne of Thunder

Siege of Orgrimmar (only the first 2 wings)

- Vale of Eternal Sorrows

- Gates of RetributionFor Secrets of the First Empire where you collect 20xSecrets of the Empire, it can drop from bosses in the following locations:

Throne of Thunder

Siege of Orgrimmar (only the first 2 wings)

- Vale of Eternal Sorrows

- Gates of RetributionFor Echoes of the Titans where you collect 12xTitan Runestone. The item can drop from: